Contacts of the helix formed by residues 488 - 499 (chain 9) in PDB entry 6FF7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 488 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4739 PRO 3.3 10.3 - - - +
4759 THR* 4.2 0.9 - - - -
4869 VAL 3.6 3.6 + - - +
4879 VAL* 1.3 76.9 - - - +
4899 LYS* 1.3 62.7 + - - +
4909 LYS 3.5 0.2 - - - -
4919 THR* 3.4 16.2 + - - +
4929 TYR* 3.0 23.7 + - - +
161X GLU* 2.8 27.8 - - + -
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Residues in contact with LYS 489 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4739 PRO* 3.8 5.5 + - + -
4759 THR* 4.2 3.6 - - - -
4889 ASN* 1.3 67.5 - - - +
4909 LYS* 1.3 39.5 - - - -
4929 TYR* 3.1 5.2 + - - +
4939 GLU 3.0 5.9 + - - -
158X LEU 3.1 0.9 - - - +
159X PRO* 1.4 33.5 - - - +
160X GLU* 1.0 162.6 + - + +
161X GLU* 1.7 13.3 - - - +
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Residues in contact with LYS 490 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4899 LYS* 1.3 57.4 - - - +
4919 THR* 1.3 43.5 + - - +
4939 GLU* 3.4 0.2 - - - +
4949 ASP* 2.9 17.7 + - - +
159X PRO* 0.9 140.7 - - - +
160X GLU 2.2 0.6 - - - +
161X GLU* 2.2 20.2 - - + +
162X THR* 2.2 53.6 - - - +
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Residues in contact with THR 491 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4879 VAL* 5.2 4.5 - - - -
4889 ASN* 3.4 25.3 + - - +
4899 LYS 3.2 0.4 - - - -
4909 LYS* 1.3 75.5 - - - +
4929 TYR* 1.3 56.7 + - - +
4949 ASP* 3.1 11.1 + - - +
4959 LEU* 3.0 25.2 + - - +
159X PRO* 1.8 4.2 - - - +
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Residues in contact with TYR 492 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4759 THR* 3.5 32.5 - - - +
4779 GLU* 5.8 7.4 - - + +
4879 VAL* 5.3 7.1 - - + +
4889 ASN 3.0 9.1 + - - +
4899 LYS 3.6 2.2 - - - +
4919 THR* 1.3 73.2 - - - +
4939 GLU* 1.3 60.4 + - - +
4959 LEU* 3.2 10.5 + - - +
4969 LYS* 2.8 25.1 + - - +
157X ASN* 4.5 0.6 - - - -
158X LEU 4.1 1.1 - - - +
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Residues in contact with GLU 493 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4899 LYS 3.0 0.2 + - - -
4909 LYS 3.4 0.2 - - - +
4929 TYR* 1.3 68.2 - - - +
4949 ASP* 1.3 56.3 + - - +
4969 LYS 3.0 0.2 + - - -
4979 ARG* 3.0 19.4 + - - +
157X ASN 1.4 30.7 - - - +
158X LEU* 1.1 87.2 + - + -
159X PRO* 1.3 29.5 - - - +
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Residues in contact with ASP 494 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4909 LYS 2.9 13.5 + - - +
4919 THR* 3.1 13.7 + - - +
4939 GLU* 1.3 75.1 - - - +
4959 LEU* 1.3 58.4 + - - +
4979 ARG* 3.3 9.9 + - - +
4989 GLN* 2.9 25.5 + - - +
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Residues in contact with LEU 495 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4919 THR 3.0 11.9 + - - +
4929 TYR* 3.2 12.3 + - - +
4949 ASP* 1.3 73.2 - - - +
4969 LYS* 1.3 55.7 + - - +
4989 GLN* 3.7 11.0 - - + +
4999 GLY* 2.8 28.8 + - - -
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Residues in contact with LYS 496 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4929 TYR 2.8 9.7 + - - +
4939 GLU 3.0 0.2 + - - -
4959 LEU* 1.3 75.8 - - - +
4979 ARG* 1.3 58.4 + - - +
4999 GLY* 3.3 19.2 + - - +
157X ASN* 0.8 87.6 - - + +
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Residues in contact with ARG 497 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4939 GLU 3.0 11.4 + - - +
4949 ASP* 3.3 11.4 + - - +
4969 LYS* 1.3 77.3 - - - +
4989 GLN* 1.3 59.8 + - - +
4999 GLY 3.9 4.0 - - - +
156X ASN 5.0 4.0 - - - +
157X ASN* 3.3 1.3 - - - +
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Residues in contact with GLN 498 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4949 ASP 2.9 15.5 + - - +
4959 LEU* 3.9 10.3 - - + +
4979 ARG* 1.3 74.8 - - - +
4999 GLY* 1.3 67.2 + - - +
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Residues in contact with GLY 499 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4959 LEU 2.8 23.3 + - - -
4969 LYS* 3.3 13.1 + - - +
4979 ARG 3.9 4.7 - - - +
4989 GLN* 1.3 79.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il